The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies

Abstract

The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods or scalability for advanced CRISPR applications. Here, we present a new ecosystem of R packages that enables efficient gRNA design and annotation for a multitude of CRISPR technologies, including CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi) and CRISPR base editing (CRISPRbe). The core package, crisprDesign, offers a comprehensive, user-friendly, and unified interface to add on- and off-target annotations via several alignment methods, rich gene and SNP annotations, and a dozen on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. We illustrate the general applicability of our tools by designing optimal gRNAs for three case studies: tiling CRISPRbe library for BRCA1 using the base editor BE4max, tiling RNA-targeting libraries for CD46 and CD55 using CasRx, and activation of MMP7 using CRISPRa. Our suite of R packages is open-source and deployed through the Bioconductor project to facilitate their use by the CRISPR community.

basilisk: a Bioconductor package for managing Python environments

“…This is more onerous but allows clients to directly call executables that are provided in the environment. For example, the crisprScore package (Hoberecht et al, 2022) relies on Python 2 environments that will no longer be supported by reticulate (Kalinowski, 2022). By directly acquiring the path to the provisioned environment, crisprScore can locate the Python 2 executable for execution of its legacy code.…”